Merge branch 'develop' into patch-1

Author: pcarruscag

.github/pull_request_template.md

@@ -12,7 +12,7 @@
 *Put an X by all that apply. You can fill this out after submitting the PR. If you have any questions, don't hesitate to ask! We want to help. These are a guide for you to know what the reviewers will be looking for in your contribution.*
 
 - [ ] I am submitting my contribution to the develop branch.
-- [ ] My contribution generates no new compiler warnings (try with the '-Wall -Wextra -Wno-unused-parameter -Wno-empty-body' compiler flags).
+- [ ] My contribution generates no new compiler warnings (try with the '-Wall -Wextra -Wno-unused-parameter -Wno-empty-body' compiler flags, or simply --warnlevel=2 when using meson).
 - [ ] My contribution is commented and consistent with SU2 style.
 - [ ] I have added a test case that demonstrates my contribution, if necessary.
 - [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp) , if necessary.

Common/include/CConfig.hpp

@@ -254,6 +254,7 @@ class CConfig {
   *Marker_Outlet,                 /*!< \brief Outlet flow markers. */
   *Marker_Isothermal,             /*!< \brief Isothermal wall markers. */
   *Marker_HeatFlux,               /*!< \brief Constant heat flux wall markers. */
+  *Marker_RoughWall,              /*!< \brief Constant heat flux wall markers. */
   *Marker_EngineInflow,           /*!< \brief Engine Inflow flow markers. */
   *Marker_EngineExhaust,          /*!< \brief Engine Exhaust flow markers. */
   *Marker_Clamped,                /*!< \brief Clamped markers. */
@@ -308,6 +309,7 @@ class CConfig {
   su2double *Outlet_Pressure;                /*!< \brief Specified back pressures (static) for outlet boundaries. */
   su2double *Isothermal_Temperature;         /*!< \brief Specified isothermal wall temperatures (static). */
   su2double *Heat_Flux;                      /*!< \brief Specified wall heat fluxes. */
+  su2double *Roughness_Height;               /*!< \brief Equivalent sand grain roughness for the marker according to config file. */
   su2double *Displ_Value;                    /*!< \brief Specified displacement for displacement boundaries. */
   su2double *Load_Value;                     /*!< \brief Specified force for load boundaries. */
   su2double *Damper_Constant;                /*!< \brief Specified constant for damper boundaries. */
@@ -555,6 +557,8 @@ class CConfig {
   *Kind_Inc_Outlet,
   *Kind_Data_Riemann,
   *Kind_Data_Giles;                /*!< \brief Kind of inlet boundary treatment. */
+  unsigned short *Kind_Wall;       /*!< \brief Type of wall treatment. */
+  unsigned short nWall_Types;      /*!< \brief Number of wall treatment types listed. */
   unsigned short nInc_Inlet;       /*!< \brief Number of inlet boundary treatment types listed. */
   unsigned short nInc_Outlet;      /*!< \brief Number of inlet boundary treatment types listed. */
   su2double Inc_Inlet_Damping;     /*!< \brief Damping factor applied to the iterative updates to the velocity at a pressure inlet in incompressible flow. */
@@ -918,7 +922,8 @@ class CConfig {
   nMarkerPitching_Ampl,           /*!< \brief Number of values provided for pitching amplitude of marker. */
   nMarkerPitching_Phase,          /*!< \brief Number of values provided for pitching phase offset of marker. */
   nMarkerPlunging_Omega,          /*!< \brief Number of values provided for angular frequency of marker. */
-  nMarkerPlunging_Ampl;           /*!< \brief Number of values provided for plunging amplitude of marker. */
+  nMarkerPlunging_Ampl,           /*!< \brief Number of values provided for plunging amplitude of marker. */
+  nRough_Wall;                    /*!< \brief Number of rough walls. */
   su2double  *Omega_HB;           /*!< \brief Frequency for Harmonic Balance Operator (in rad/s). */
   unsigned short
   nOmega_HB,                      /*!< \brief Number of frequencies in Harmonic Balance Operator. */
@@ -991,7 +996,9 @@ class CConfig {
   DV_Penalty;                       /*!< \brief Penalty weight to add a constraint to the total amount of stiffness. */
   unsigned long Nonphys_Points,     /*!< \brief Current number of non-physical points in the solution. */
   Nonphys_Reconstr;                 /*!< \brief Current number of non-physical reconstructions for 2nd-order upwinding. */
-  bool ParMETIS;                    /*!< \brief Boolean for activating ParMETIS mode (while testing). */
+  su2double ParMETIS_tolerance;     /*!< \brief Load balancing tolerance for ParMETIS. */
+  long ParMETIS_pointWgt;           /*!< \brief Load balancing weight given to points. */
+  long ParMETIS_edgeWgt;            /*!< \brief Load balancing weight given to edges. */
   unsigned short DirectDiff;        /*!< \brief Direct Differentation mode. */
   bool DiscreteAdjoint,                  /*!< \brief AD-based discrete adjoint mode. */
   FullTape;                              /*!< \brief Full tape mode for coupled discrete adjoints. */
@@ -1077,7 +1084,8 @@ class CConfig {
   default_body_force[3],         /*!< \brief Default body force vector for the COption class. */
   default_nacelle_location[5],   /*!< \brief Location of the nacelle. */
   default_hs_axes[3],            /*!< \brief Default principal axes (x, y, z) of the ellipsoid containing the heat source. */
-  default_hs_center[3];          /*!< \brief Default position of the center of the heat source. */
+  default_hs_center[3],          /*!< \brief Default position of the center of the heat source. */
+  default_roughness[1];
 
   unsigned short Riemann_Solver_FEM;         /*!< \brief Riemann solver chosen for the DG method. */
   su2double Quadrature_Factor_Straight;      /*!< \brief Factor applied during quadrature of elements with a constant Jacobian. */
@@ -2924,6 +2932,12 @@ class CConfig {
    */
   unsigned short GetnMarker_HeatFlux(void) const { return nMarker_HeatFlux; }
 
+  /*!
+   * \brief Get the total number of rough markers.
+   * \return Total number of heat flux markers.
+   */
+  unsigned short GetnRoughWall(void) const { return nRough_Wall; }
+
   /*!
    * \brief Get the total number of objectives in kind_objective list
    * \return Total number of objectives in kind_objective list
@@ -5004,6 +5018,11 @@ class CConfig {
    */
   unsigned short GetKind_ActDisk(void) const { return Kind_ActDisk; }
 
+  /*!
+   * \brief Set the kind of wall - rough or smooth.
+   */
+  void SetKindWall(string val_marker, unsigned short val_kindwall);
+
   /*!
    * \brief Get the number of sections.
    * \return Number of sections
@@ -6754,6 +6773,13 @@ class CConfig {
    */
   su2double* GetWallFunction_DoubleInfo(string val_marker);
 
+  /*!
+   * \brief Get the type of wall and roughness height on a wall boundary (Heatflux or Isothermal).
+   * \param[in] val_index - Index corresponding to the boundary.
+   * \return The wall type and roughness height.
+   */
+  pair<unsigned short, su2double> GetWallRoughnessProperties(string val_marker) const;
+
   /*!
    * \brief Get the target (pressure, massflow, etc) at an engine inflow boundary.
    * \param[in] val_index - Index corresponding to the engine inflow boundary.
@@ -9360,6 +9386,21 @@ class CConfig {
    */
   unsigned long GetEdgeColoringGroupSize(void) const { return edgeColorGroupSize; }
 
+  /*!
+   * \brief Get the ParMETIS load balancing tolerance.
+   */
+  passivedouble GetParMETIS_Tolerance() const { return SU2_TYPE::GetValue(ParMETIS_tolerance); }
+
+  /*!
+   * \brief Get the ParMETIS load balancing weight for points.
+   */
+  long GetParMETIS_PointWeight() const { return ParMETIS_pointWgt; }
+
+  /*!
+   * \brief Get the ParMETIS load balancing weight for edges
+   */
+  long GetParMETIS_EdgeWeight() const { return ParMETIS_edgeWgt; }
+
   /*!
    * \brief Find the marker index (if any) that is part of a given interface pair.
    * \param[in] iInterface - Number of the interface pair being tested, starting at 0.

Common/include/fem/fem_geometry_structure.hpp

@@ -880,7 +880,7 @@ class CMeshFEM_DG: public CMeshFEM {
   * \brief Set the send receive boundaries of the grid.
   * \param[in] config - Definition of the particular problem.
   */
-  void SetSendReceive(CConfig *config) override;
+  void SetSendReceive(const CConfig *config) override;
 
   /*!
    * \brief Set the local index that correspond with the global numbering index.

Common/include/geometry/CGeometry.hpp

@@ -137,8 +137,8 @@ class CGeometry {
 
 #if defined(HAVE_MPI) && defined(HAVE_PARMETIS)
   vector<vector<unsigned long> > adj_nodes; /*!< \brief Vector of vectors holding each node's adjacency during preparation for ParMETIS. */
-  idx_t *adjacency{nullptr}; /*!< \brief Local adjacency array to be input into ParMETIS for partitioning (idx_t is a ParMETIS type defined in their headers). */
-  idx_t *xadj{nullptr};      /*!< \brief Index array that points to the start of each node's adjacency in CSR format (needed to interpret the adjacency array).  */
+  vector<idx_t> adjacency; /*!< \brief Local adjacency array to be input into ParMETIS for partitioning (idx_t is a ParMETIS type defined in their headers). */
+  vector<idx_t> xadj;      /*!< \brief Index array that points to the start of each node's adjacency in CSR format (needed to interpret the adjacency array).  */
 #endif
 
   /*--- Turbomachinery variables ---*/
@@ -769,7 +769,7 @@ class CGeometry {
    * \brief A virtual member.
    * \param[in] config - Definition of the particular problem.
    */
-  inline virtual void SetColorGrid_Parallel(CConfig *config) {}
+  inline virtual void SetColorGrid_Parallel(const CConfig *config) {}
 
   /*!
    * \brief A virtual member.
@@ -789,7 +789,7 @@ class CGeometry {
    * \param[in] config - Definition of the particular problem.
    * \param[in] val_domain - Number of domains for parallelization purposes.
    */
-  inline virtual void SetSendReceive(CConfig *config) {}
+  inline virtual void SetSendReceive(const CConfig *config) {}
 
   /*!
    * \brief A virtual member.

Common/include/geometry/CPhysicalGeometry.hpp

@@ -31,6 +31,7 @@
 #include "meshreader/CMeshReaderFVM.hpp"
 #include "../toolboxes/C2DContainer.hpp"
 
+
 /*!
  * \class CPhysicalGeometry
  * \brief Class for reading a defining the primal grid which is read from the grid file in .su2 or .cgns format.
@@ -105,6 +106,9 @@ class CPhysicalGeometry final : public CGeometry {
   unsigned long *Elem_ID_BoundTria_Linear{nullptr};
   unsigned long *Elem_ID_BoundQuad_Linear{nullptr};
 
+  vector<int> GlobalMarkerStorageDispl;
+  vector<su2double> GlobalRoughness_Height;
+
 public:
   /*--- This is to suppress Woverloaded-virtual, omitting it has no negative impact. ---*/
   using CGeometry::SetVertex;
@@ -160,22 +164,22 @@ class CPhysicalGeometry final : public CGeometry {
    * \param[in] geometry - Definition of the geometry container holding the initial linear partitions of the grid + coloring.
    * \param[in] config - Definition of the particular problem.
    */
-  void DistributeColoring(CConfig *config, CGeometry *geometry);
+  void DistributeColoring(const CConfig *config, CGeometry *geometry);
 
   /*!
    * \brief Distribute the grid points, including ghost points, across all ranks based on a ParMETIS coloring.
    * \param[in] config - Definition of the particular problem.
    * \param[in] geometry - Geometrical definition of the problem.
    */
-  void DistributePoints(CConfig *config, CGeometry *geometry);
+  void DistributePoints(const CConfig *config, CGeometry *geometry);
 
   /*!
    * \brief Distribute the connectivity for a single volume element type across all ranks based on a ParMETIS coloring.
    * \param[in] config - Definition of the particular problem.
    * \param[in] geometry - Geometrical definition of the problem.
    * \param[in] Elem_Type - VTK index of the element type being distributed.
    */
-  void DistributeVolumeConnectivity(CConfig *config, CGeometry *geometry, unsigned short Elem_Type);
+  void DistributeVolumeConnectivity(const CConfig *config, CGeometry *geometry, unsigned short Elem_Type);
 
   /*!
    * \brief Distribute the connectivity for a single surface element type in all markers across all ranks based on a ParMETIS coloring.
@@ -269,21 +273,17 @@ class CPhysicalGeometry final : public CGeometry {
    * \brief Routine to sort the adjacency for ParMETIS for graph partitioning in parallel.
    * \param[in] config - Definition of the particular problem.
    */
-  void SortAdjacency(CConfig *config);
+  void SortAdjacency(const CConfig *config);
 
   /*!
    * \brief Set the send receive boundaries of the grid.
-   * \param[in] geometry - Geometrical definition of the problem.
    * \param[in] config - Definition of the particular problem.
-   * \param[in] val_domain - Number of domains for parallelization purposes.
    */
-  void SetSendReceive(CConfig *config) override;
+  void SetSendReceive(const CConfig *config) override;
 
   /*!
    * \brief Set the send receive boundaries of the grid.
-   * \param[in] geometry - Geometrical definition of the problem.
    * \param[in] config - Definition of the particular problem.
-   * \param[in] val_domain - Number of domains for parallelization purposes.
    */
   void SetBoundaries(CConfig *config) override;
 
@@ -369,7 +369,7 @@ class CPhysicalGeometry final : public CGeometry {
    * \brief Prepares the grid point adjacency based on a linearly partitioned mesh object needed by ParMETIS for graph partitioning in parallel.
    * \param[in] config - Definition of the particular problem.
    */
-  void PrepareAdjacency(CConfig *config);
+  void PrepareAdjacency(const CConfig *config);
 
   /*!
    * \brief Find repeated nodes between two elements to identify the common face.
@@ -529,7 +529,7 @@ class CPhysicalGeometry final : public CGeometry {
    * \brief Set the domains for grid grid partitioning using ParMETIS.
    * \param[in] config - Definition of the particular problem.
    */
-  void SetColorGrid_Parallel(CConfig *config) override;
+  void SetColorGrid_Parallel(const CConfig *config) override;
 
   /*!
    * \brief Set the domains for FEM grid partitioning using ParMETIS.
@@ -804,4 +804,9 @@ class CPhysicalGeometry final : public CGeometry {
     }
   }
 
+  /*!
+   * \brief Set roughness values for markers in a global array.
+   */
+  void SetGlobalMarkerRoughness(const CConfig* config);
+
 };

Common/include/geometry/dual_grid/CPoint.hpp

@@ -85,6 +85,7 @@ class CPoint {
   su2activevector SharpEdge_Distance;     /*!< \brief Distance to a sharp edge. */
   su2activevector Curvature;              /*!< \brief Value of the surface curvature (SU2_GEO). */
   su2activevector MaxLength;              /*!< \brief The maximum cell-center to cell-center length. */
+  su2activevector RoughnessHeight;          /*!< \brief Roughness of the nearest wall. */
 
   su2matrix<int> AD_InputIndex;           /*!< \brief Indices of Coord variables in the adjoint vector. */
   su2matrix<int> AD_OutputIndex;          /*!< \brief Indices of Coord variables in the adjoint vector after having been updated. */
@@ -400,6 +401,20 @@ class CPoint {
    */
   inline su2double GetWall_Distance(unsigned long iPoint) const { return Wall_Distance(iPoint); }
 
+  /*!
+   * \brief Set the value of the distance to the nearest wall.
+   * \param[in] iPoint - Index of the point.
+   * \param[in] distance - Value of the distance.
+   */
+  inline void SetRoughnessHeight(unsigned long iPoint, su2double roughheight) { RoughnessHeight(iPoint) = roughheight; }
+
+  /*!
+   * \brief Get the value of the distance to the nearest wall.
+   * \param[in] iPoint - Index of the point.
+   * \return Value of the distance to the nearest wall.
+   */
+  inline su2double GetRoughnessHeight(unsigned long iPoint) const { return RoughnessHeight(iPoint); }
+
   /*!
    * \brief Set the value of the distance to a sharp edge.
    * \param[in] iPoint - Index of the point.

Common/include/geometry/dual_grid/CTurboVertex.hpp

@@ -117,7 +117,7 @@ class CTurboVertex final : public CVertex {
    * \brief get global index for ordered span-wise turbovertex.
    */
   inline int GetGlobalVertexIndex(void) const {return GlobalIndex;}
- 
+
   /*!
    * \brief set angular coord.
    */

Common/include/mpi_structure.hpp

@@ -50,21 +50,16 @@
 #include <medi/medi.hpp>
 using namespace medi;
 
+#include <codi/externals/codiMpiTypes.hpp>
+
 class CMediMPIWrapper;
 typedef CMediMPIWrapper SU2_MPI;
 
-#if defined CODI_REVERSE_TYPE
-#include <codi/externals/codiMediPackTypes.hpp>
-#if CODI_PRIMAL_INDEX_TAPE
-typedef CoDiPackToolPrimalRestore<su2double> MediTool;
-#else
-typedef CoDiPackTool<su2double> MediTool;
-#endif // defined CODI_REVERSE_TYPE
-#elif defined CODI_FORWARD_TYPE
-#include <codi/externals/codiForwardMediPackTypes.hpp>
-typedef CoDiPackForwardTool<su2double> MediTool;
-#endif // defined CODI_FORWARD_TYPE
-#define AMPI_ADOUBLE ((medi::MpiTypeInterface*)MediTool::MPI_TYPE)
+typedef CoDiMpiTypes<su2double> MediTypes;
+typedef MediTypes::Tool MediTool;
+
+extern MediTypes* mediTypes;
+#define AMPI_ADOUBLE ((medi::MpiTypeInterface*)mediTypes->MPI_TYPE)
 
 #else
 class CBaseMPIWrapper;
@@ -417,7 +412,7 @@ class CBaseMPIWrapper {
                         void *recvbuf, int recvcnt, Datatype recvtype, Comm comm);
 
   static void Allgatherv(void *sendbuf, int sendcnt, Datatype sendtype,
-                         void *recvbuf, int recvcnt, int *displs, Datatype recvtype, Comm comm);
+                         void *recvbuf, int *recvcnt, int *displs, Datatype recvtype, Comm comm);
 
   static void Sendrecv(void *sendbuf, int sendcnt, Datatype sendtype,
                        int dest, int sendtag, void *recvbuf, int recvcnt,

Common/include/mpi_structure.inl

@@ -286,7 +286,7 @@ inline passivedouble CBaseMPIWrapper::Wtime(void) {
 
 inline void CMediMPIWrapper::Init(int *argc, char ***argv) {
   AMPI_Init(argc,argv);
-  MediTool::init();
+  mediTypes = new MediTypes();
   AMPI_Comm_rank(convertComm(currentComm), &Rank);
   AMPI_Comm_size(convertComm(currentComm), &Size);
 
@@ -298,7 +298,7 @@ inline void CMediMPIWrapper::Init(int *argc, char ***argv) {
 
 inline void CMediMPIWrapper::Init_thread(int *argc, char ***argv, int required, int* provided) {
   AMPI_Init_thread(argc,argv,required,provided);
-  MediTool::init();
+  mediTypes = new MediTypes();
   AMPI_Comm_rank(convertComm(currentComm), &Rank);
   AMPI_Comm_size(convertComm(currentComm), &Size);
 
@@ -310,7 +310,7 @@ inline void CMediMPIWrapper::Init_thread(int *argc, char ***argv, int required,
 
 inline void CMediMPIWrapper::Init_AMPI(void) {
   AMPI_Init_common();
-  MediTool::init();
+  mediTypes = new MediTypes();
 }
 
 inline void CMediMPIWrapper::SetComm(Comm newComm){
@@ -391,6 +391,8 @@ inline void CMediMPIWrapper::Comm_size(Comm comm, int *size){
 
 inline void CMediMPIWrapper::Finalize(){
   if( winMinRankErrorInUse ) MPI_Win_free(&winMinRankError);
+
+  delete mediTypes;
   AMPI_Finalize();
 }
 
@@ -612,7 +614,7 @@ inline void CBaseMPIWrapper::Scatter(void *sendbuf, int sendcnt, Datatype sendty
 }
 
 inline void CBaseMPIWrapper::Allgatherv(void *sendbuf, int sendcnt, Datatype sendtype,
-                                   void *recvbuf, int recvcnt, int *displs, Datatype recvtype, Comm comm){
+                                   void *recvbuf, int *recvcnt, int *displs, Datatype recvtype, Comm comm){
   CopyData(sendbuf, recvbuf, sendcnt, sendtype);
 }
 

Common/include/option_structure.hpp

@@ -1394,6 +1394,18 @@ static const MapType<string, ACTDISK_TYPE> ActDisk_Map = {
   MakePair("VARIABLE_LOAD", VARIABLE_LOAD)
 };
 
+/*!
+ * \brief types of wall boundary condition - smooth or rough
+ */
+enum WALL_TYPE {
+  SMOOTH = 1,    /*!< \brief Smooth wall */
+  ROUGH = 2,   /*!< \brief Rough wall */
+};
+static const MapType<string, WALL_TYPE> WallType_Map = {
+  MakePair("SMOOTH", SMOOTH)
+  MakePair("ROUGH", ROUGH)
+};
+
 /*!
  * \brief Types of geometric entities based on VTK nomenclature
  */